TY - GEN
T1 - Pseudo-dihedral Angles in Proteins Providing a New Description of the Ramachandran Map
AU - Da Rocha, Wagner
AU - Lavor, Carlile
AU - Liberti, Leo
AU - Malliavin, Thérèse E.
N1 - Publisher Copyright:
© 2023, The Author(s), under exclusive license to Springer Nature Switzerland AG.
PY - 2023/1/1
Y1 - 2023/1/1
N2 - Since the first years of structural biology, the Ramachandran map has provided a simple definition of the curvilinear geometry of the protein backbone. Its definition is mainly based on the values of the dihedral angles ϕ and ψ measured between the heavy atoms of the protein backbone. Discontinuities in angle values are observed, particularly in the region of the β -strand secondary structure. We introduce new pseudo-dihedral angles involving hydrogen positions instead of some of the positions of the heavy atoms. We determine simple relationships between the old and new dihedral angles. We show that combining the old and new parameters allows us to overcome the discontinuity problem encountered in the Ramachandran map.
AB - Since the first years of structural biology, the Ramachandran map has provided a simple definition of the curvilinear geometry of the protein backbone. Its definition is mainly based on the values of the dihedral angles ϕ and ψ measured between the heavy atoms of the protein backbone. Discontinuities in angle values are observed, particularly in the region of the β -strand secondary structure. We introduce new pseudo-dihedral angles involving hydrogen positions instead of some of the positions of the heavy atoms. We determine simple relationships between the old and new dihedral angles. We show that combining the old and new parameters allows us to overcome the discontinuity problem encountered in the Ramachandran map.
KW - Ramachandran map
KW - interval Branch-and-Prune
KW - pseudo-dihedral angles
U2 - 10.1007/978-3-031-38299-4_53
DO - 10.1007/978-3-031-38299-4_53
M3 - Conference contribution
AN - SCOPUS:85173443775
SN - 9783031382987
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 511
EP - 519
BT - Geometric Science of Information - 6th International Conference, GSI 2023, Proceedings
A2 - Nielsen, Frank
A2 - Barbaresco, Frédéric
PB - Springer Science and Business Media Deutschland GmbH
T2 - The 6th International Conference on Geometric Science of Information, GSI 2023
Y2 - 30 August 2023 through 1 September 2023
ER -